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Making FinalSurf edits

Here we will look at the second time point ( OAS2_0002_MR2).

In the brain.finalsurfs.mgz volume (your aux volume in tkmedit) you can see the pial surface encroaching into the cerebellum in slices 65 - 68: Representative slice 68 shown below, problem at coordinates 111 136 68 in right hemisphere

Zoomed in version is below

First make a copy of this volume to one called 'brain.finalsurfs.manedit.mgz' and save it within the mri directory of this time point, along with the other volumes.

cp OAS2_0002_MR2/mri/brain.finalsurfs.mgz OAS2_0002_MR2/mri/brain.finalsurfs.manedit.mgz

Next, load the brain.finalsurfs.manedit.mgz volume as the aux volume in tkmedit and edit this volume by going through the affected slices and removing the voxels in the cerebellum and surrounding areas that cause the pial surface misplacement. Once you are finished editing, save the changes to the volume with File – Save Aux volume.

Next, run the following to have the edits take effect:

recon-all -subjid OAS2_0002_MR2 -autorecon3-pial 

The results will look as follows, (see OAS2_0002_MR2_fixed) : Notice how the pial surface is now pulled in based on the deleted voxels

Zoomed in version

Next, it is time to fix the base for this subject - return to the Longitudinal Tutorial to see how.